A method is provided for transferring a substrate from a first substrate holder, e.g., a pre-alignment unit, to a second substrate holder, e.g., a substrate table in a lithographic apparatus, by means of a transfer unit on the basis of transfer data available thereto. First, the substrate is provided on the first substrate holder. Subsequently, a position error of the substrate is measured, and positioning adjustment data are calculated based on the position error as measured. Then, the second substrate holder is moved relative to a reference position thereof in accordance with the positioning adjustment data. Finally, the substrate is transferred by means of the transfer unit from the first substrate holder to the second substrate holder in accordance with the transfer data, and placed on the second substrate holder as moved.